Digging on problem with keybindings not working in PhpStorm IDE, I tried several Java applications and realized that keybindings with letter keys are not working in Swing/AWT applications on my linux machine at all.

Problem is that in PhpStorm (which is a Java Swing application), keyboard shortcuts containing letter keys like Ctrl+X are not working, resulting in 'Unknown keyCode: 0x0' error in settings dialog, though shortcuts not containing letter keys like Ctrl+Space are working ok.

I am not alone with such problem, there is at least one more person, who created an issue at PhpStorm bugtracker (I am not allowed to post third link in this post, but you can find issue IDEA-75450 in Google)

I am not a Java programmer, but as I understood, the problem does not depend on JRE and desktop environment, it lies somewhere between Swing/AWT and linux.